Related papers: Towards Experimental P-systems using multivesicula…
This paper introduces a new method to perform signal processing using cells or atoms to synthesize variation in digital data stored in optical format. Interfacing small-scale biological or chemical systems with information stored on CD, DVD…
Membrane computing is a branch of natural computingwhich abstracts fromthe structure and the functioning of living cells. The computation models obtained in the field of membrane computing are usually called P systems. P systems have been…
The cell membrane is inherently asymmetric and heterogeneous in its composition, a feature that is crucial for its function. Using atomistic molecular dynamics simulations, the physical properties of a 3-component asymmetric mixed lipid…
Nature is remarkably adept at using interfaces to build structures, encapsulate reagents, and regulate biological processes. Inspired by Nature, we describe flexible polymer-based ribbons, termed "mesoscale polymers" (MSPs), to modulate…
Room-temperature metals and semi-metals which consist of a gas of bound electrons in a near-continuum band structure can be classified as cold quantum plasmas. This insight suggests that Particle-in-Cell (PIC) simulations, traditionally…
Continuous latent variables (LVs) are a key ingredient of many generative models, as they allow modelling expressive mixtures with an uncountable number of components. In contrast, probabilistic circuits (PCs) are hierarchical discrete…
Multilamellar wall vesicles (MLWV) are an interesting class of polyelectrolyte-surfactant complexes (PESCs) for wide applications ranging from house-care to biomedical products. If MLWV are generally obtained by a polyelectrolyte-driven…
In the post-Moore era, the need for efficient solutions to non-deterministic polynomial-time (NP) problems is becoming more pressing. In this context, the Ising model implemented by the probabilistic computing systems with probabilistic…
A coarse-grained model developed by Marrink et al. [J. Phys. Chem. B 111, 7812 (2007)] is applied to investigate vesiculation of lipid [dipalmitoylphosphatidylcholine (DPPC)] droplets in water. Three kinds of morphologies of micelles are…
Volume of fluid (VOF) methods are extensively used to track fluid interfaces in numerical simulations, and many VOF algorithms require that the interface be reconstructed geometrically. For this purpose, the Piecewise Linear Interface…
A stochastic model is used to assess the effect of external parameters on the development of submerged biofilms on smooth and rough surfaces. The model includes basic cellular mechanisms, such as division and spreading, together with an…
In this paper we present an extension of standard iterative splitting schemes to multiple splitting schemes for solving higher order differential equations. We are motivated by dynamical systems, which occur in dynamics of the electrons in…
Ribosomes are critical biomolecular nanomachines responsible for protein synthesis in all known organisms. The function and dynamics of ribosomes can be studied using molecular dynamics computer simulations. Although this task remains…
We present an extensive molecular dynamics (MD) simulation study of poly(ethylene oxide) (PEO) based densely cross-linked polymers, focussing on structural properties as well as the systems dynamics in the presence of lithium salt.…
Phantom systems consisting of liposome suspensions are widely employed to investigate quantitative MRI parameters mimicking cellular membranes. The proper physical understanding of the measurement results, however, requires proper models…
Recently proposed modifications of the standard particle-in-cell (PIC) method resolve long-standing limitations such as exact preservation of physically conserved quantities and unbiased ensemble down-sampling. Such advances pave the way…
The variational discrete element method developed in [28] for dynamic elasto-plastic computations is adapted to compute the deformation of elastic Cosserat materials. In addition to cellwise displacement degrees of freedom (dofs), cellwise…
Voronoi tessellations of Poisson point processes are widely used for modeling many types of physical and biological systems. In this paper, we analyze simulated Poisson-Voronoi structures containing a total of 250,000,000 cells to provide…
The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…
A general framework to describe a vast majority of biology-inspired systems is to model them as stochastic processes in which multiple couplings are in play at the same time. Molecular motors, chemical reaction networks, catalytic enzymes,…